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bfactor specifications

Information


Unique identifier OMICS_26901
Name bfactor
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0.4
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Nikolaus Grigorieff

bfactor citations

 (28)
library_books

Tubulin isoform composition tunes microtubule dynamics

2017
Mol Biol Cell
PMCID: 5706985
PMID: 29021343
DOI: 10.1091/mbc.E17-02-0124

[…] verfitting during refinement using a high-resolution noise-substitution test (). Using local resolution estimates determined with the blocres program in Bsoft, the reconstruction was sharpened with a Bfactor of −180 up to a resolution of 5.5 or 4 Å for visualization of kinesin or tubulin densities respectively. […]

library_books

Cryo EM structure of the protein conducting ERAD channel Hrd1 in complex with Hrd3

2017
Nature
PMCID: 5736104
PMID: 28682307
DOI: 10.1038/nature23314

[…] ement procedures and the FSC=0.143 criterion. Local resolution was estimated using Resmap . The amplitude information of the final maps was corrected by applying a negative B-factor using the program bfactor.exe .To speed up calculations, the cryo-EM data set (871,530 particles) was divided into two halves for the initial round of 3D classification. No symmetry was applied unless otherwise indicat […]

library_books

Linear epitope prediction in HPV type 16 E7 antigen and their docked interaction with human TMEM 50A structural model

2017
Bioinformation
PMCID: 5498776
PMID: 28690376
DOI: 10.6026/97320630013122

[…] other in the protein model and is used for making decision about its reliability. ERRAT showed an overall quality factor of 31.544, a result expected for crystallographic models with resolution>2.5A. Bfactor analysis is done with WHAT IF server reflected the mobility or flexibility of various parts of the molecule. Averaged B-factor deviation for protein backbone was 0.082 (Z score mean) and avera […]

call_split

Ensemble cryo EM elucidates the mechanism of translation fidelity

2017
Nature
PMCID: 5657493
PMID: 28538735
DOI: 10.1038/nature22397
call_split See protocol

[…] ed classes III and IIIb, which only differ in the L11 stalk occupancy, as described above).The maps used for structure refinements were sharpened by applying negative B-factors of up to −100 Å2 using bfactor.exe (included with the FREALIGN distribution). FSC curves were calculated by FREALIGN for even and odd particle half-sets. frealign_calc_stats was used to derive the number of particles assign […]

call_split

Cryo EM structure of human adenovirus D26 reveals the conservation of structural organization among human adenoviruses

2017
Sci Adv
PMCID: 5425241
PMID: 28508067
DOI: 10.1126/sciadv.1602670
call_split See protocol

[…] Frealign 3D maps, which were generated with a box size of 1200 pixels3. Multiple sharpened maps, obtained by applying different negative temperature factors (−100, −150, and −200 Å2 using the program bfactor.exe), along with the unsharpened map, were used for model building. […]

library_books

Cryo EM structures reveal specialization at the myosin VI actin interface and a mechanism of force sensitivity

2017
eLife
PMCID: 5762158
PMID: 29199952
DOI: 10.7554/eLife.31125.058

[…] e FSC 0.143 criterion () as 4.6 Å (rigor), 5.5 Å (ADP), and 5 Å (actin alone) (). The maps were sharpened using a B-factor peaking at the nominal average resolution as indicated in using the program BFACTOR.Local resolution assessment was performed in two independent fashions. Since it was clear that the resolution decayed radially from the core of the filament, we calculated a series of reconstr […]

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